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EnsMart: a generic system for fast and flexible access to biological data
Arek Kasprzyk1, Damian Keefe, Damian Smedley
1European Bioinformatics Institute (EBI), Hinxton, Cambridge CB10 1SH, UK. arek@ebi.ac.uk
Genome Research
|January 7, 2004
Summary
EnsMart offers a flexible data warehousing system for biological research, enabling efficient querying and integration of large datasets. This system supports diverse research needs, from gene screening to evolutionary comparisons, with customizable data retrieval options.
Area of Science:
- Bioinformatics
- Genomics
- Data Management
Background:
- Biological datasets are large and complex, requiring efficient management and querying.
- Integrating diverse biological data and third-party tools is a significant challenge for researchers.
Purpose of the Study:
- To introduce EnsMart, a generic data warehousing solution for biological data.
- To enhance the Ensembl genomic browser's capabilities for data retrieval and analysis.
Main Methods:
- Developed a query-optimized database with interactive user interfaces.
- Applied the EnsMart system to the Ensembl platform.
- Enabled dynamic generation of data in various formats (HTML, text, Excel, compressed).
Main Results:
- EnsMart facilitates fast and flexible querying of large biological datasets.
- Supports complex queries on various annotations across multiple species.
- Enables customized data retrieval for diverse research applications, including SNP selection, evolutionary comparisons, and microarray annotation.
- Allows grouping and refining data by criteria like cross-species analyses, disease links, sequence variations, and expression patterns.
- Provides retrieval of various sequence types (cDNA, peptides, exons) with flanking regions.
Conclusions:
- EnsMart provides a powerful and adaptable solution for biological data warehousing and analysis.
- The system is freely available for public access and local installation, supporting 'non-Ensembl' datasets.